https://github.com/4ment/sts-test
https://github.com/4ment/sts-test
Last synced: 8 months ago
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- Host: GitHub
- URL: https://github.com/4ment/sts-test
- Owner: 4ment
- License: gpl-3.0
- Created: 2018-06-06T23:39:53.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2018-06-08T09:09:15.000Z (about 8 years ago)
- Last Synced: 2024-12-27T04:42:25.953Z (over 1 year ago)
- Language: C++
- Size: 8.86 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
Sequential Tree Sampler (STS)
=============================
The sequential tree sampler implements a prototype of online phylogenetics, updating a posterior distribution generated by MrBayes with new sequences.
The algorithm has been described and its performance evaluated in [a manuscript][preprint].
The scripts used to generate the figures can be found [here](https://github.com/OnlinePhylo/sts-online-experiments).
## Dependencies
* [smctc][smctc] - included as git submodule (`git submodule update --init`)
* [lcfit][lcfit] - included as git submodule (`git submodule update --init`)
* [Bio++ version 2.2.0][bpp] `core`, `seq`, and `phyl` modules. Note that debian & ubuntu up to 16.04 include v2.1.0 which is too old. Bio++ should be installed from source using the `bpp-setup.sh` script on these systems.
* [cmake][cmake]
* [gsl version 1.16][gsl] Note that gsl v2 is not currently supported.
* [nlopt][nlopt]
* [beagle][beagle] version 2.1 (Optional)
* [google test][gtest] this is libgtest on debian/ubuntu (Optional)
## Compiling
1. Install dependencies
2. run `make`
Binaries will be build in `_build/release`
## Adding taxa to an existing posterior
The tool `sts-online` adds taxa to an existing posterior tree sample.
`sts-online` operates on a fasta file and tree file in nexus format.
The fasta file must contain an alignment with a superset of the taxa in the tree file.
Currently only the Jukes-Cantor model is supported.
### Example invocation
sts-online -b 250 -p 2 --proposal-method lcfit 10taxon-01.fasta 10tax_trim_t1.t 10tax_trim_t1.sts.json
In this example, we use an alignment containing 10 sequences and a posterior sample of trees generated by MrBayes with an alignment that does not contain the sequence labeled `t1`.
`sts-online` ignores the first 250 trees from `50tax_trim.run1.t` and uses a particle factor of 2. The `10tax_trim_t1.sts.json` file will contain the updated trees.
[preprint]: http://biorxiv.org/content/early/2017/06/02/145219
[smctc]: http://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/johansen/smctc/
[lcfit]: http://github.com/matsengrp/lcfit/
[beagle]: https://code.google.com/p/beagle-lib/
[bpp]: http://biopp.univ-montp2.fr/
[cmake]: http://www.cmake.org/
[gsl]: https://www.gnu.org/software/gsl/
[nlopt]: http://ab-initio.mit.edu/wiki/index.php/NLopt
[gtest]: https://github.com/google/googletest